From 187e1277c00f4ce25b496fc8a9f0d986e9870512 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Jun 2020 08:47:34 +0200
Subject: [PATCH] update sambamba memory requirements and parameter_meta
---
sambamba.wdl | 37 ++++++++++++++++++++++++++++++-------
1 file changed, 30 insertions(+), 7 deletions(-)
diff --git a/sambamba.wdl b/sambamba.wdl
index 4ef62dd..bf58dbc 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -25,18 +25,23 @@ task Markdup {
input {
Array[File] inputBams
String outputPath
- Int threads = 1
+ # Sambamba scales like this: 1 thread is fully utilized (1). 2 threads 1.8 utilized. 3 -> 2.4, 4-> 2.7.
+ # 2 threads reduces wall clock time by more than 40%.
+ Int threads = 2
Int compressionLevel = 1
Int? hashTableSize
Int? overFlowListSize
- Int? sortBufferSize
- Int? ioBufferSize
+ # sortBufferSize and ioBufferSize taken from markdup defaults as of sambamba 0.7.1
+ Int sortBufferSize = 2048
+ Int ioBufferSize = 128
Boolean removeDuplicates = false
- # According to the manual sambamba markdup uses about 2G per 100 million reads.
- Int memoryGb = 1 + ceil(size(inputBams, 'G') / 8)
+ # According to the manual sambamba markdup uses the sortbufferSize + 2 times the ioBuffer size.
+ # Added 1024 mb as a margin of safety
+ Int memoryMb = 1024 + sortBufferSize + 2 * ioBufferSize
String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
- Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8)
+ # Time minute calculation does not work well for higher number of threads.
+ Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8) / threads
}
String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
@@ -62,11 +67,29 @@ task Markdup {
}
runtime {
- memory: "~{memoryGb}G"
+ memory: "~{memoryMb}M"
cpu: threads
time_minutes: timeMinutes
docker: dockerImage
}
+
+ parameter_meta {
+ # inputs
+ inputBams: {description: "The input BAM files.", category: "required"}
+ outputPath: {description: "Output directory path + output file.", category: "required"}
+ compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
+ memoryMb: {description: "The amount of memory available to the job in megabytes.", category: "advanced"}
+ removeDuplicates: {description: "Whether to remove the duplicates (instead of only marking them).", category: "advanced"}
+ hashTableSize: {description: "Sets sambamba's hash table size", category: "advanced"}
+ overFlowListSize: {description: "Sets sambamba's overflow list size", category: "advanced"}
+ sortBufferSize: {description: "The amount of mb allocated to the sort buffer", category: "advanced"}
+ ioBufferSize: {description: "The amount of mb allocated to each IO buffer. Sambamba uses two IO buffers.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ # outputs
+ outputBam: {description: "Sorted BAM file."}
+ }
}
task Sort {
--
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